2.4 Sequence analysis
Nucleotide compositional skew was calculated according to the formulae:
AT-skew = (A−T)/(A+T) and GC-skew = (G−C)/(G+C) [42]. The Sequence
Manipulation Suite program package
(http://www.bioinformatics.org/sms2/codon_usage.html) was used to
analyze codon usage based on genetic code “4” [43]. Genetic
distances between each pair of the 14 core PCGs (atp6, atp8, atp9,
cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad4L, nad5, andnad6 ) were calculated with MEGA X [44], using the
Kimura−2-parameter (K2P) substitution model. DnaSP v6 [45] was used
to calculate the nonsynonymous (Ka) and synonymous (Ks) substitution
rates for the 14 core PCGs among the four mitogenomes. Genomic synteny
among the four mitogenomes was analyzed using the Mauve v2.4.0 program
[46].